Adelie Penguins Project

Summary

• Context
  • This project belongs to Santiago Florimonte’s portfolio, and is part of saint_analytics, a business idea in the making.
• What you’ll find
  • Facts and visuals about Adelie penguins
  • R code used to make the visuals (click the ’ code ’ button at the right side of the visuals to check it out)
  • Tables containing datasets for the visuals, sources, and credits

Lets find out about Adelie Penguins!

These fancy birds live in settlements - known as colonies - all around the Antarctica coast.

Their calendar year consists of 2 seasons:

• Breeding season, during warmer months (October to February), when they get a small window to beget and socialize in their lifelong colonies.
• Foraging season, which begins in mid-February, as Adelies leave the colonies to hunt all over packed-ice waters in the antarctic sea until heat returns to the south and they can breed again.

Adelies are relatively small and slow compared to other penguins, but they still survive in hostile conditions at the southern pole. This makes them a crucial subject of environmental research.

Some definitions before moving on to the visuals, so that you don’t have to google them

• Creche: A cumulation of penguin chicks.
• Forage: To wander or go around in search of provisions.
• Waddle: To walk with short steps, swaying or rocking from side to side, as a duck or penguin.

Adelie snapshot: context and visuals

Adelies among penguins

ggplot(Peng_body_plotdf) +
  geom_point(aes(x =Peng_nm, y = Peng_ht), size = 2) +
  draw_image(img_ad, x = 0.5, y = 10, height = 40, scale = 1.5) +
  draw_image(img_ch, x = 1.4, y = 10, height = 45, scale = 1.5) +
  draw_image(img_emp, x = 2.5, y = 15, height = 83, scale = 1.5) +
  draw_image(img_ge, x = 3.5, y = 10, height = 50, scale = 1.5) +
  scale_y_continuous(limits = c(1,145), breaks = c(seq(0,160,40))) +
  labs(title = "Comparing Adelies to other penguins", 
       subtitle = "(numbers represent averages)", y = "Height (cm)", x = NULL) + theme_classic() +
  theme(axis.ticks.y = element_line(linewidth = 0), 
        axis.text = element_text(size = 14), 
        panel.grid.major.y = element_line(color = 'grey', linewidth = .25), 
        plot.title = element_text(size = 18, face = 'bold', hjust = 0),
        plot.subtitle = element_text(size = 14, face = 'bold', hjust = 0),
        plot.margin = unit(c(2.5, 1, 1, 1), "lines")) +
  annotation_custom(img_saint_1 %>% rasterGrob(), 
                    xmin=3.7, xmax=4.5, ymin=147, ymax=177) +
  coord_cartesian(clip = "off") +
  annotate("text", label = Peng_body_plotdf$summ  ,
           x = Peng_body_plotdf$x_coord, y = Peng_body_plotdf$y_coord, color = "black", 
           size = 9/.pt, hjust = 0) +
  annotate("segment", x = seq(0.6,3.6, 1), xend = seq(1, 4, 1), 
           y = Peng_body_plotdf$Peng_ht, yend = Peng_body_plotdf$Peng_ht, 
           color = "black", linewidth = 2/.pt) +
  annotate("segment", x = seq(0.6,3.6, 1), xend = seq(0.6,3.6, 1), 
           y = Peng_body_plotdf$Peng_ht, yend = c(82, 92, 142, 97), 
           color = "black", linewidth = 2/.pt)

Additional info

Things Adelies share with other penguins

• Diet, and predators with the rest of the penguins shown above…
  • They all eat Antarctic silverfish, Krill (Adelies favorite), Squid, and sometimes Jellyfish.
  • They are victims of evil creatures such as Killer whales, Leopard seals, and giant birds like Skuas or Sheathbills. Birds being the worst of all, targeting chicks exclusively.
• Bondage - as kindship - with Chinstraps and Gentoos.
• Antarctica’s ownership with the Emperors: These 2 are the only penguins who live exclusively on the continent.

What sets Adelies apart

• Our little fellas are the slowest of the viz. On land, they waddle at a speed of 2.5 km/h. On the water, Adelies reach a maximum of 8km/h.
• It’s hard to differentiate males from females, even for them.
• Adelies are known for being “dangerously” curious, feisty, and selfish creatures.

Fun Facts

• Selfish animals…
  “At the place where they most often went in [the water], a long terrace of ice about six feet in height ran for some hundreds of yards along the edge of the water, and here, just as on the sea ice, crowds would stand near the brink. When they had succeeded in pushing one of their number over, all would crane their necks over the edge, and when they saw the pioneer safe in the water, the rest followed.” - George Murray Levick, British Royal Navy Surgeon-Lieutenant and Scientist (1910).
• Feisty reputation: They’re well known for fighting off predators, and even slap (yes, slap) researchers on the ground.
• Showcasing Adelies attitude:
  • Protecting young ones.
  • Slapping, not researchers, unfortunately.
  • Stealing from others (conduct shared with other species).

---

Antarctica: Home of Adelies

ggplot(colonies_2tr_df) +
  geom_sf(data = st_transform(ne_countries(
    continent = c("Antarctica"), returnclass = "sf")), fill="#FFFFFF") +
   geom_sf(alpha = .8, mapping = aes(fill = ccamlr_reg_abs, shape = ccamlr_reg_abs), 
          size = 2, color = "black") + 
  scale_shape_manual(name = "CCAMLR Regions", values = c(21,22,23)) +
  scale_fill_manual(name = "CCAMLR Regions", 
                    values = c("#3399FF", "#336666", "#999999")) +
  labs(title = "Adelie colonies",
       subtitle = "Colonies recorded from the 80's up to date", 
       caption = "CCAMLR: Commision for the Conservation of Antarctica Marine Living Resources.") +
  theme(panel.background = element_rect(fill="lightblue"),
        title = element_text(size = 14, face = 'bold', hjust = 0),
        plot.subtitle = element_text(size = 14, face = 'bold', hjust = 0), 
        plot.caption = element_text(size = 10),
        legend.title = element_text(size = 10),
        plot.margin = unit(c(2.5, 1, 1, 1), "lines")) +
  annotation_custom(img_saint_1 %>% rasterGrob(), 
                    xmin=3200000, xmax=4800000, ymin=-1900000, ymax=-700000) +
  coord_sf(clip = "off")

kbl(pop_table, format.args = list(big.mark = ","), align = "c") %>% 
  kable_styling(full_width = F, bootstrap_options = "striped") %>%  
  column_spec(3, color = ifelse(pop_table$`Most frequent counting accuracy` > 1, 
                                "red", "green"), width = "4cm") %>% 
  column_spec(4, color = ifelse(pop_table$`Most frequent counting accuracy` > 1, 
                                "red", "green"), width = "4cm") %>% 
  row_spec(0, bold = T ) %>% 
  row_spec(4, bold = T ) %>% 
  footnote("'Penguin count only considers penguins or nests in the colonies at the time of counting.\nvhr: Very High Quality. Refering to image resolution of pictures taken from alternative counting methods.", footnote_as_chunk = T, 
           general_title = " ")

Region	Penguin count	Most frequent counting method	Most frequent counting accuracy	Colonies (n)
48	1,459,896	ground	1	102
58	1,098,313	vhr	5	85
88	1,761,649	aerial	2	58
Antarctica	4,319,858	vhr	5	245
’Penguin count only considers penguins or nests in the colonies at the time of counting. vhr: Very High Quality. Refering to image resolution of pictures taken from alternative counting methods.

Additional info

• Adelies live in the coldest and most isolated place on earth. Such conditions make it difficult to get information on them. Finding new colonies, or updating on located ones is a big challenge, so it is to update population counts.
• They are censused from the following vantages:
  • At ground level.
  • On the air with drones or helicopters.
  • On the water on vessels.
  • From out of space with satelites.
• The counting process itself consists of a literal count of penguins or nests, either by hand - “1, 2, 3, 4, 5…” - or by approximation via supervised classification, which means that a computer counts them from a picture, with a certain margin of error.
• Newborns forage for a few years before returning to their colonies.
  These adventurers were excluded from the table. If included, Adelies’ population would almost double according to the International Union for the Conservation of Nature (IUCN).
• An example of dynamics in penguins research in general, is the recent finding of one of the largest colonies currently known for Adelies. Located in Danger islands, in the Antarctic Peninsula, these colonies were casually identified in NASA satellite imagery in 2014. By the end of 2015, an international research group went to the location to confirm the presence of hundreds of thousands of Adelies.
  This finding meant more than just adding colonies to a list: It changed a decreasing tendency of the species population.

---

Adelies breeding

ggplot(join_breeding_plotdf) + 
  geom_point(aes(x = laps, y = groups), color = "white") +
  geom_segment(data = arrow_ref_breedingplot, 
               aes(x = x, xend = xend, y = y, yend = yend), 
           color = "#3399CC",
           size = 20, linejoin = c('mitre'),
           arrow = arrow(angle = 30, length = unit(0.4,'inches'))) +
  geom_curve(data = curve_ref_breedingplot, aes(x = 5.1, y = 4, xend = 4.8, yend = 3.5), 
             color = "#3399CC",
             curvature = -.5, size = 20, lineend = c('square')) +
  geom_curve(data = curve_ref_breedingplot, aes(x = 4.75, y = 1.5, xend = 5.1, yend = 0.9), 
             color = "#3399CC",
             curvature = -.5, size = 20, lineend = c('butt')) +
  annotate("text", label = breed_summ_plotdf$summ  ,
           x = breed_summ_plotdf$x_coord, y = breed_summ_plotdf$y_coord, color = "black", 
           size = 3.5, hjust = 0) +
  annotate("text", label = rep("Forage season", 2)  ,
           x = c(5.1, 5.1), y = c(4.4, 0.3), color = "#3399CC", 
           size = 5, fontface = "bold") +
  draw_image(img_ad_c1, x = 3.6, y = 2.6, height = 1.3) +
  draw_image(img_ad_c2, x = 1.8, y = 2.8, height = 1.1) +
  draw_image(img_ad_c3a, x = 0.2, y = 3, height = .8) +
  draw_image(img_ad_c4a, x = 0.2, y = 0.9, height = .9) +
  draw_image(img_ad_c5, x = 1.8, y = 0.85, height = .9) + 
  draw_image(img_ad_c6, x = 3.7, y = 0.8, height = 1.3) +
  scale_y_continuous(limits = c(0.2,4.5)) + 
  scale_x_continuous(limits = c(.5,5.25), name = '') +
  labs(title = "Adelies breeding cycle",
       subtitle = " ") +
  theme(panel.background = element_rect(fill = "white"), 
        title = element_text(size = 16, face = 'bold', hjust = 0), 
        plot.caption = element_text(size = 10),
        axis.ticks = element_blank(), axis.text = element_blank(), 
        axis.title = element_blank(), axis.line.x.top = element_line(linewidth = 2), 
        panel.border = element_rect(colour = "grey", fill = NA, linewidth = .5),
        plot.margin = unit(c(2.5, 1, 1, 1), "lines")) +
  annotation_custom(img_saint_1 %>% rasterGrob(), 
                    xmin=4.2, xmax=5.6, ymin=4.72, ymax=5.34) +
  coord_cartesian(clip = "off")

Additional info

• Adults return to the same colony every year for their breeding season after foraging during the winter.
• Pebble nests are built with the best pebbles males can find or steal from others. The quality of picked pebbles is a relevant factor for females when choosing a mate.
• Critical period between incubation and Creches: Parents take turns looking after babies and feeding expeditions. If a parent leaves the colony for too long, the other one either leaves babies on their own - unprotected from freezing temperatures and predators - or starve to death. This period wipes out more than a third of Adelie chicks.
• Newborns don’t return to the colony until they reach adulthood (3 to 5 years).
• Adelies remember and return to tested and proven nests in later years.

---

Appendix

---

imagery credits

# Table of 12 rows, 2 columns: c(Article Tag, credit)

reactable(
  img_cred, pagination = FALSE, highlight = TRUE, height = 175, 
  columns = list(
   # Use raw HTML
    imagery_tag = colDef(name = "Image label"),
    imagery_credit = colDef(name = "Credits (w/link)", html = TRUE, 
                            cell = function(value, index) {
      sprintf('<a href="%s" target="_blank">%s</a>', img_cred$imagery_link[index], value)
    }), 
    imagery_link = colDef(show = F) 
  )
)

---

sources

# Table of n rows, 2 columns: c(Name, links "source link")

reactable(
  sou_lk, pagination = FALSE, highlight = TRUE, height = 175, 
  columns = list(
   # Use raw HTML
    source = colDef(name = "Source"),
    access = colDef(name = "Source Access", html = TRUE, 
                            cell = function(value, index) {
      sprintf('<a href="%s" target="_blank">%s</a>', sou_lk$source_link[index], value)
    }), 
    source_link = colDef(show = F) 
  )
)

---

data sets

• Comparison dataset

Peng_body_plotdf %>% datatable(rownames = F, 
                              extensions = 'Buttons',
                              options = list(dom = 'Blfrtip',
                                             buttons = c('copy', 'csv', 'excel'), 
                           pageLength = 4, lengthMenu = c(1, 2, 4)))

• Maps dataset

colonies_2tr_df %>% datatable(rownames = F, 
                              extensions = 'Buttons',
                              options = list(dom = 'Blfrtip',
                                             buttons = c('copy', 'csv', 'excel'), 
                           pageLength = 4, lengthMenu = c(4, 8, 12)))